1. What are proteins? Proteins are important; e.g. for catalyzing and regulating biochemical reactions, transporting molecules, … Linear polymer chain composed of tens (peptides) to thousands (proteins) of monomers Monomers are 20 naturally occurring amino acids Different proteins have different amino acid sequences Structureless, extended unfolded state Compact, ‘unique’ native folded state (with secondary and tertiary structure) required for biological function Sequence determines protein structure (or lack thereof) Proteins unfold or denature with increasing temperature or chemical denaturants Linear polymerFolded state 1

2. Amino Acids I N-terminalC-terminal CC variable side chain R peptide bonds Side chains differentiate amino acid repeat units Peptide bonds link residues into polypeptides 2

3. Amino Acids II 3

4. The Protein Folding Problem: What is ‘ unique ’ folded 3D structure of a protein based on its amino acid sequence? Sequence  Structure Lys-Asn-Val-Arg-Ser-Lys-Val-Gly-Ser-Thr-Glu-Asn-Ile-Lys- His-Gln-Pro- Gly-Gly-Gly-… 4

5. Folding: hydrophobicity, hydrogen bonding, van der Waals interactions, … Unfolding: increase in conformational entropy, electric charge… H (hydrophobic) P (polar) inside outside Hydrophobicity index Driving Forces 5

6. Van der Waals interactions – hydrogen bonds – covalent bonds 5-12 k b TkbTkbT> 150 k b T

7. Secondary Structure: Loops,  -helices,  -strands/sheets  -sheet  -strand Right-handed; three turns Vertical hydrogen bonds between NH 2 (teal/white) backbone group and C=O (grey/red) backbone group four residues earlier in sequence Side chains (R) on outside; point upwards toward NH 2 Each amino acid corresponds to 100 , 1.5Å, 3.6 amino acids per turn ( ,  )=(-60 ,-45  )  -helix propensities: Met, Ala, Leu, Glu  -helix 5-10 residues; peptide backbones fully extended NH (blue/white) of one strand hydrogen-bonded to C=O (black/red) of another strand C ,side chains (yellow) on adjacent strands aligned; side chains along single strand alternate up and down ( ,  )=(-135 ,135  )  -strand propensities: Val, Thr, Tyr, Trp, Phe, Ile 5Å 7

8. Bond Lengths and Angles Leu dipeptide C’ i-1 N CαCα C’C’ N i+1

9. Leu τ

12. Backbonde Dihedral Angles 12

13. Ramachandran Plot: Determining Steric Clashes C  CN’C’  NC  CN’ Backbone dihedral angles    =0,180  Non-Gly Gly theory PDB   vdW radii < vdW radii backbone flexibility 4 atoms define dihedral angle: 13

14. C’ i-1 ‘ ϕ : C’ i-1 NC α C’ ψ: NC α C’N i+1 ω 1 :C i-1 α C’ i-1 NC α ω 2 :C α C’N i+1 C i+1 α G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, “Stereochemistry of polypeptide chain Configurations,” J. Mol. Biol. 7 (1963) 95.

15. Backbone dihedral angles from PDB

16. 16

17. Side-Chain Dihedral Angles Side chain: C  -CH 2 -CH 2 -CH 2 -CH 2 -NH 3  4 : Lys, Arg  5 : Arg Use NC  C  C  C  C  N  to define  1,  2,  3,  4 17

18. Side Chain Dihedral Angles Leu dipeptide C’ i-1 N CαCα C’C’ N i+1

19. Sidechain Dihedral Angle Distributions for Leu PDB

20. Folding Transition T>T m T<T m Oxygen: Red Carbon: Cyan Nitrogen: Dark Blue Sulfur: Yellow

21. Why do proteins fold (correctly & rapidly)??  = # allowed dihedral angles How does a protein find the global optimum w/o global search? Proteins fold much faster. For a protein with N amino acids, number of backbone conformations/minima Levinthal ’ s paradox: N c ~ 3 200 ~10 95  fold ~ N c  sample ~10 83 s  universe ~ 10 17 s vs  fold ~ 10 -6 -10 -3 s 21

22. U, F =U-TS Energy Landscape all atomic coordinates; dihedral angles M1M1 M3M3 M2M2 S 12 S 23 S -1 minimum saddle point maximum 22

23. Roughness of Energy Landscape smooth, funneled rough (Wolynes et. al. 1997) 23